There were plenty of indicators, and perhaps a President less absorbed in his own glorious self would have paid them some attention. And a Cabinet and Executive Branch appointees with at least a minimum of competence might have been helpful, too.
As it is, the Clinton Administration is going to go down as one of the most incompetent in history- and probably one of the 2 or 3 most corrupt.
They can repeat it all they want, but it won't work, because it's already been proven untrue. Sure, he couldn't have forseen that event X was going to happen precisely on 9/11/2001 yadda yadda, but we already have mountains of evidence that the Clintoons were given many many warnings over time of Al Qaida's rampups; that the Clintoons baldly passed on several opportunities to have Bin Laden handed over to the US on a silver platter; etc etc. At this point, there is essentially no doubt that 9/11 would not have happened if only Bill Clinton had bothered to take action on any of a number of options made easily available to him during his term of office.
At best (for him), history will convict Bill Clinton of reckless endangerment and/or reckless disregard for the safety of the nation. My guess is the eventual verdict will be somewhat more harsh than that.